cqm-reports 2.1.1 → 3.0.0.pre.alpha.1

data/lib/qrda-import/data-element-importers/procedure_recommended_importer.rb

@@ -7,7 +7,6 @@ module QRDA
         @code_xpath = "./cda:code"
         @author_datetime_xpath = "./cda:author/cda:time"
         @anatomical_location_site_xpath = "./cda:targetSiteCode"
-        @ordinality_xpath = "./cda:priorityCode"
         @reason_xpath = "./cda:entryRelationship[@typeCode='RSON']/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.88']/cda:value"
         @entry_class = QDM::ProcedureRecommended
       end
@@ -15,7 +14,6 @@ module QRDA
       def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
         procedure_recommended = super
         procedure_recommended.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
-        procedure_recommended.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
         procedure_recommended.reason = extract_reason(entry_element)
         procedure_recommended
       end

data/lib/qrda-import/entry_package.rb

@@ -0,0 +1,16 @@
+module QRDA
+  module Cat1
+    class EntryPackage
+
+      attr_accessor :importer_type
+
+      def initialize(type)
+        self.importer_type = type
+      end  
+
+      def package_entries(doc, nrh)
+        importer_type.create_entries(doc, nrh)
+      end
+    end
+  end
+end

data/lib/qrda-import/patient_importer.rb

@@ -12,117 +12,88 @@ module QRDA
       def initialize
         # This differs from other HDS patient importers in that sections can have multiple importers
         @data_element_importers = []
-        @data_element_importers << AdverseEventImporter.new
-        @data_element_importers << AllergyIntoleranceImporter.new
-        @data_element_importers << AssessmentOrderImporter.new
-        @data_element_importers << AssessmentPerformedImporter.new
-        @data_element_importers << AssessmentRecommendedImporter.new
-        @data_element_importers << CommunicationPerformedImporter.new
-        @data_element_importers << DeviceAppliedImporter.new
-        @data_element_importers << DeviceOrderImporter.new
-        @data_element_importers << DeviceRecommendedImporter.new
-        @data_element_importers << DiagnosisImporter.new
-        @data_element_importers << DiagnosticStudyOrderImporter.new
-        @data_element_importers << DiagnosticStudyPerformedImporter.new
-        @data_element_importers << DiagnosticStudyRecommendedImporter.new
-        @data_element_importers << EncounterOrderImporter.new
-        @data_element_importers << EncounterPerformedImporter.new
-        @data_element_importers << EncounterRecommendedImporter.new
-        @data_element_importers << FamilyHistoryImporter.new
-        @data_element_importers << ImmunizationAdministeredImporter.new
-        @data_element_importers << ImmunizationOrderImporter.new
-        @data_element_importers << InterventionOrderImporter.new
-        @data_element_importers << InterventionPerformedImporter.new
-        @data_element_importers << InterventionRecommendedImporter.new
-        @data_element_importers << LaboratoryTestOrderImporter.new
-        @data_element_importers << LaboratoryTestPerformedImporter.new
-        @data_element_importers << LaboratoryTestRecommendedImporter.new
-        @data_element_importers << MedicationActiveImporter.new
-        @data_element_importers << MedicationAdministeredImporter.new
-        @data_element_importers << MedicationDischargeImporter.new
-        @data_element_importers << MedicationDispensedImporter.new
-        @data_element_importers << MedicationOrderImporter.new
-        @data_element_importers << PatientCareExperienceImporter.new
-        @data_element_importers << PatientCharacteristicClinicalTrialParticipantImporter.new
-        @data_element_importers << PatientCharacteristicExpiredImporter.new
-        @data_element_importers << PatientCharacteristicPayerImporter.new
-        @data_element_importers << PhysicalExamOrderImporter.new
-        @data_element_importers << PhysicalExamPerformedImporter.new
-        @data_element_importers << PhysicalExamRecommendedImporter.new
-        @data_element_importers << ProcedureOrderImporter.new
-        @data_element_importers << ProcedurePerformedImporter.new
-        @data_element_importers << ProcedureRecommendedImporter.new
-        @data_element_importers << ProviderCareExperienceImporter.new
-        @data_element_importers << ProviderCharacteristicImporter.new
-        @data_element_importers << SubstanceAdministeredImporter.new
-        @data_element_importers << SubstanceOrderImporter.new
-        @data_element_importers << SubstanceRecommendedImporter.new
-        @data_element_importers << SymptomImporter.new
+        @data_element_importers << generate_importer(AdverseEventImporter)
+        @data_element_importers << generate_importer(AllergyIntoleranceImporter)
+        @data_element_importers << generate_importer(AssessmentOrderImporter)
+        @data_element_importers << generate_importer(AssessmentPerformedImporter)
+        @data_element_importers << generate_importer(AssessmentRecommendedImporter)
+        @data_element_importers << generate_importer(CommunicationPerformedImporter)
+        @data_element_importers << generate_importer(DeviceAppliedImporter)
+        @data_element_importers << generate_importer(DeviceOrderImporter)
+        @data_element_importers << generate_importer(DeviceRecommendedImporter)
+        @data_element_importers << generate_importer(DiagnosisImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyOrderImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyPerformedImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyRecommendedImporter)
+        @data_element_importers << generate_importer(EncounterOrderImporter)
+        @data_element_importers << generate_importer(EncounterPerformedImporter)
+        @data_element_importers << generate_importer(EncounterRecommendedImporter)
+        @data_element_importers << generate_importer(FamilyHistoryImporter)
+        @data_element_importers << generate_importer(ImmunizationAdministeredImporter)
+        @data_element_importers << generate_importer(ImmunizationOrderImporter)
+        @data_element_importers << generate_importer(InterventionOrderImporter)
+        @data_element_importers << generate_importer(InterventionPerformedImporter)
+        @data_element_importers << generate_importer(InterventionRecommendedImporter)
+        @data_element_importers << generate_importer(LaboratoryTestOrderImporter)
+        @data_element_importers << generate_importer(LaboratoryTestPerformedImporter)
+        @data_element_importers << generate_importer(LaboratoryTestRecommendedImporter)
+        @data_element_importers << generate_importer(MedicationActiveImporter)
+        @data_element_importers << generate_importer(MedicationAdministeredImporter)
+        @data_element_importers << generate_importer(MedicationDischargeImporter)
+        @data_element_importers << generate_importer(MedicationDispensedImporter)
+        @data_element_importers << generate_importer(MedicationOrderImporter)
+        @data_element_importers << generate_importer(PatientCareExperienceImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicClinicalTrialParticipantImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicExpiredImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicPayerImporter)
+        @data_element_importers << generate_importer(PhysicalExamOrderImporter)
+        @data_element_importers << generate_importer(PhysicalExamPerformedImporter)
+        @data_element_importers << generate_importer(PhysicalExamRecommendedImporter)
+        @data_element_importers << generate_importer(ProcedureOrderImporter)
+        @data_element_importers << generate_importer(ProcedurePerformedImporter)
+        @data_element_importers << generate_importer(ProcedureRecommendedImporter)
+        @data_element_importers << generate_importer(ProviderCareExperienceImporter)
+        @data_element_importers << generate_importer(SubstanceAdministeredImporter)
+        @data_element_importers << generate_importer(SubstanceOrderImporter)
+        @data_element_importers << generate_importer(SubstanceRecommendedImporter)
+        @data_element_importers << generate_importer(SymptomImporter)
       end 
 
       def parse_cat1(doc)
         patient = CQM::Patient.new
-        warnings = []
-        codes_modifiers = {}
         entry_id_map = {}
-        import_data_elements(patient, doc, entry_id_map, codes_modifiers, warnings)
+        import_data_elements(patient, doc, entry_id_map)
         normalize_references(patient, entry_id_map)
         get_demographics(patient, doc)
-        [patient, warnings, codes_modifiers]
+        patient
       end
 
-      def import_data_elements(patient, doc, entry_id_map, codes_modifiers, warnings = [])
+      def import_data_elements(patient, doc, entry_id_map)
         context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
         nrh = NarrativeReferenceHandler.new
         nrh.build_id_map(doc)
-        @data_element_importers.each do |importer|
-          data_elements, id_map = importer.create_entries(context, nrh)
+        @data_element_importers.each do |entry_package|
+          data_elements, id_map = entry_package.package_entries(context, nrh)
           new_data_elements = []
 
           id_map.each_value do |elem_ids|
+            
             elem_id = elem_ids.first
             data_element = data_elements.find { |de| de.id == elem_id }
-            # Keep the first element with a shared ID
-            new_data_elements << data_element
-
-            # Encounters require elements beyond id for uniqueness
-            next unless data_element._type == 'QDM::EncounterPerformed'
-            unique_element_keys = []
-            # Add key_elements_for_determining_encounter_uniqueness to array, this is used to determine if other
-            # elements with the same ID should be considered as unique
-            unique_element_keys << key_elements_for_determining_encounter_uniqueness(data_element)
 
-            # Loop through all other data elements with the same id
-            elem_ids[1,elem_ids.length].each do |dup_id|
-              dup_element = data_elements.find { |de| de.id == dup_id }
-              dup_element_keys = key_elements_for_determining_encounter_uniqueness(dup_element)
-              # See if a previously selected data element shared all of the keys files
-              # If all key fields match, move on.
-              next if unique_element_keys.include?(dup_element_keys)
-              # If all key fields don't match, keep element
-              new_data_elements << dup_element
-              # Add to list of unique element keys
-              unique_element_keys << dup_element_keys
+            elem_ids[1,elem_ids.length].each do |merge_id|
+              merge_element = data_elements.find { |de| de.id == merge_id }
+              data_element.merge!(merge_element)
             end
+
+            new_data_elements << data_element
           end
 
           patient.qdmPatient.dataElements << new_data_elements
           entry_id_map.merge!(id_map)
-          warnings.concat(importer.warnings)
-          codes_modifiers.merge!(importer.codes_modifiers)
-          # reset warnings after they're captured so that the importer can be re-used
-          importer.warnings = []
-          importer.codes_modifiers = {}
         end
       end
 
-      def key_elements_for_determining_encounter_uniqueness(encounter)
-        codes = encounter.codes.collect { |dec| "#{dec.code}_#{dec.codeSystemOid}" }.sort.to_s
-        admission_date_time = encounter&.relevantPeriod&.low.to_s
-        discharge_date_time = encounter&.relevantPeriod&.high.to_s
-        "#{codes}#{admission_date_time}#{discharge_date_time}"
-      end
-
       def get_patient_expired(record, doc)
         entry_elements = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']/cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
         return unless entry_elements.empty?
@@ -145,6 +116,12 @@ module QRDA
           end
         end
       end
+
+      private
+
+      def generate_importer(importer_class)
+        EntryPackage.new(importer_class.new)
+      end
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cqm-reports
 version: !ruby/object:Gem::Version
-  version: 2.1.1
+  version: 3.0.0.pre.alpha.1
 platform: ruby
 authors:
 - The MITRE Corporation
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-09-11 00:00:00.000000000 Z
+date: 2019-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: cqm-models
@@ -16,28 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 3.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 2.0.0
-- !ruby/object:Gem::Dependency
-  name: cqm-validators
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 2.0.0
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 3.0.0
 - !ruby/object:Gem::Dependency
   name: mustache
   requirement: !ruby/object:Gem::Requirement
@@ -70,16 +56,16 @@ dependencies:
   name: mongoid-tree
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
@@ -160,7 +146,9 @@ files:
 - Gemfile
 - README.md
 - Rakefile
-- lib/cqm_report.rb
+- lib/cqm-reports.rb
+- lib/ext/code.rb
+- lib/ext/data_element.rb
 - lib/html-export/qdm-patient/_header_css.mustache
 - lib/html-export/qdm-patient/_javascript.mustache
 - lib/html-export/qdm-patient/data_element/_data_element.mustache
@@ -224,7 +212,6 @@ files:
 - lib/qrda-export/catI-r5/qrda_templates/procedure_performed.mustache
 - lib/qrda-export/catI-r5/qrda_templates/procedure_recommended.mustache
 - lib/qrda-export/catI-r5/qrda_templates/provider_care_experience.mustache
-- lib/qrda-export/catI-r5/qrda_templates/provider_characteristic.mustache
 - lib/qrda-export/catI-r5/qrda_templates/substance_recommended.mustache
 - lib/qrda-export/catI-r5/qrda_templates/symptom.mustache
 - lib/qrda-export/catI-r5/qrda_templates/template_partials/_admission_source.mustache
@@ -314,12 +301,12 @@ files:
 - lib/qrda-import/data-element-importers/procedure_performed_importer.rb
 - lib/qrda-import/data-element-importers/procedure_recommended_importer.rb
 - lib/qrda-import/data-element-importers/provider_care_experience_importer.rb
-- lib/qrda-import/data-element-importers/provider_characteristic_importer.rb
 - lib/qrda-import/data-element-importers/substance_administered_importer.rb
 - lib/qrda-import/data-element-importers/substance_order_importer.rb
 - lib/qrda-import/data-element-importers/substance_recommended_importer.rb
 - lib/qrda-import/data-element-importers/symptom_importer.rb
 - lib/qrda-import/entry_finder.rb
+- lib/qrda-import/entry_package.rb
 - lib/qrda-import/narrative_reference_handler.rb
 - lib/qrda-import/patient_importer.rb
 - lib/util/code_system_helper.rb
@@ -345,12 +332,11 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: A library for import and export of reports for use with electronic Clinical

data/lib/qrda-export/catI-r5/qrda_templates/provider_characteristic.mustache

@@ -1,15 +0,0 @@
-<entry>
-  <observation classCode="OBS" moodCode="EVN">
-    <!-- Provider Characteristic Observation Assertion (V3) -->
-    <templateId root="2.16.840.1.113883.10.20.24.3.114" extension="2017-08-01"/>
-    <id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
-    <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4" codeSystemName="HL7ActCode" />
-    <statusCode code="completed" />
-    <!-- Provider Characteristic -->
-    {{> qrda_templates/template_partials/_data_element_codes_as_values}}
-    {{#authorDatetime}}
-      <!-- QDM Attribute: Author dateTime -->
-      {{> qrda_templates/template_partials/_author}}
-    {{/authorDatetime}}
-  </observation>
-</entry>

data/lib/qrda-import/data-element-importers/provider_characteristic_importer.rb

@@ -1,19 +0,0 @@
-module QRDA
-  module Cat1
-    class ProviderCharacteristicImporter < SectionImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.114']"))
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = "./cda:value"
-        @author_datetime_xpath = "./cda:author/cda:time"
-        @entry_class = QDM::ProviderCharacteristic
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        provider_characteristic = super
-        provider_characteristic
-      end
-
-    end
-  end
-end